Please fill out the fields below so we can help you better. Note: you must provide your domain name to get help. Domain names for issued certificates are all made public in Certificate Transparency logs (e.g. https://crt.sh/?q=example.com), so withholding your domain name here does not increase secrecy, but only makes it harder for us to provide help.

It produced this output:
it installed letsenrypt successfully
My web server is (include version): nginx

The operating system my web server runs on is (include version):
ubunto 17.10
My hosting provider, if applicable, is:linode.com
I can login to a root shell on my machine (yes or no, or I don’t know):
yes
I’m using a control panel to manage my site (no, or provide the name and version of the control panel): no, i use shell

I installed for one domain name but now all the rest of the websites that are configured under the same nginx are not working. they seem to be directed to the same domain name which i installed the certificate for:https://properties.fatpalm.com/

I installed for one domain name but now all the rest of the websites that are configured under the same nginx are not working. they seem to be directed to the same domain name which i installed the certificate for:

With certonly you would have had to install the certificate yourself by editing the nginx configuration file; did you do that, and what kind of modifications did you make to your nginx configuration? Could you share the nginx configuration here?

okay,
I have a nodejs api process hosted on the domain properties.fatpalm.com and that is using a 443 port.
so when i restarted the node service , the website worked back again (properties.fatpalm.com) and stopped (the access) the other websites!

Yes, this is very important. A common configuration would be to use the nginx proxy_pass directive to make nginx forward connections to the Node.js process on the local machine. This works well for most cases where you have a Node.js web application with general static web content served by nginx and with HTTPS handled by the nginx service.

thanks everyone, @schoen@rg305
when a front end messes up with back end, crazy things happen!
I was configuring both nginx and node with the same ports 443!
So i made a bypass proxy on nginx and it worked like a charm.

Hey, I’m glad that turned out to be the problem! Feel free to suggest this idea to other Node devs you may know if they’re wondering about HTTPS, because it seems like this is becoming a very popular solution. (nginx gives you a lot of power on the HTTPS side, if you want it, and the proxy_pass method gives you the ability to develop pretty much all of the application logic in Node.)